Cyclic di-GMP Signaling in the Phytopathogen Xanthomonas campestris pv. campestris

  • Ya-Wen HeEmail author
  • Wei Qian
  • Shan-Ho Chou


Xanthomonas campestris pv. campestris (Pammel) Dowson (Xcc hereafter) is the causal agent of black rot of crucifers. Whole genome sequencing has revealed an abundance of GGDEF-, EAL-, and HD-GYP-domain-containing proteins in Xcc. Most GGDEF, EAL, and HD-GYP domains are linked to a wide range of signal-input domains, suggesting that numerous environmental and internal signals can be potentially integrated into the cyclic di-GMP metabolism network. This chapter summarizes these interesting findings with a focus on diffusible signaling factor (DSF)-dependent quorum sensing, RavS/RavR-dependent hypoxia sensing and the identified cyclic di-GMP effectors in Xcc.


Xanthomonas campestris Cyclic di-GMP RpfG RavR Clp YajQ 


  1. 1.
    Williams PH (1980) Black rot: a continuing threat to world crucifers. Plant Dis 64(8):736–742. CrossRefGoogle Scholar
  2. 2.
    Vicente JG, Holub EB (2013) Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to Brassica crops. Mol Plant Pathol 14(1):2–18. CrossRefPubMedGoogle Scholar
  3. 3.
    Onsando JM (1992) Black rot of crucifers. In: Chaube HS, Kumar J, Mukhopadhyay AN, Singh US (eds) Diseases of vegetables and oil seed crops, vol 2. Prentice Hall, Upper Saddle River, pp 243–252Google Scholar
  4. 4.
    Hugouvieux V, Barber CE, Daniels MJ (1998) Entry of Xanthomonas campestris pv. campestris into hydathodes of Arabidopsis thaliana leaves: a system for studying early infection events in bacterial pathogenesis. Mol Plant-Microbe Interact 11(6):537–543. CrossRefPubMedGoogle Scholar
  5. 5.
    Yun MH, Torres PS, Oirdi ME, Rigano LA, Gonzalez-Lamothe R, Marano MR, Castagnaro AP, Dankert MA, Bouarab K, Vojnov AA (2006) Xanthan induces plant susceptibility by suppressing callose deposition. Plant Physiol 141(1):178–187. CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Torres PS, Malamud F, Rigano LA, Russo DM, Marano MR, Castagnaro AP, Zorreguieta A, Bouarab K, Dow JM, Vojnov AA (2007) Controlled synthesis of the DSF cell–cell signal is required for biofilm formation and virulence in Xanthomonas campestris. Environ Microbiol 9(8):2101–2109. CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Canonne J, Marino D, Jauneau A, Pouzet C, Brière C, Roby D, Rivas S (2011) The Xanthomonas type III effector XopD targets the arabidopsis transcription factor Myb30 to suppress plant defense. Plant Cell 23(9):3498–3511. CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    He YW, Wu J, Zhou L, Yang F, He YQ, Jiang BL, Bai L, Xu Y, Deng Z, Tang JL, Zhang LH (2011) Xanthomonas campestris diffusible factor is 3-hydroxybenzoic acid and is associated with xanthomonadin biosynthesis, cell viability, antioxidant activity, and systemic invasion. Mol Plant-Microbe Interact 24(8):948–957. CrossRefPubMedGoogle Scholar
  9. 9.
    Cao X-Q, Wang J-Y, Zhou L, Chen B, Jin Y, He Y-W (2018) Biosynthesis of the yellow xanthomonadin pigments involves an ATP-dependent 3-hydroxybenzoic acid: acyl carrier protein ligase and an unusual type II polyketide synthase pathway. Mol Microbiol 110(1):16–32. CrossRefPubMedGoogle Scholar
  10. 10.
    Poplawsky AR, Urban SC, Chun W (2000) Biological role of xanthomonadin pigments in Xanthomonas campestris pv. campestris. Appl Environ Microbiol 66(12):5123–5127CrossRefGoogle Scholar
  11. 11.
    Zhou L, Wang J-Y, Wang J, Poplawsky A, Lin S, Zhu B, Chang C, Zhou T, Zhang L-H, He Y-W (2013) The diffusible factor synthase XanB2 is a bifunctional chorismatase that links the shikimate pathway to ubiquinone and xanthomonadins biosynthetic pathways. Mol Microbiol 87(1):80–93. CrossRefPubMedGoogle Scholar
  12. 12.
    Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, Dow M, Verdier V, Beer SV, Machado MA, Toth I, Salmond G, Foster GD (2012) Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol 13(6):614–629. CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    He Y-W, Chou S-H (2016) Cyclic di-GMP regulation in plant-pathogenic bacteria. In: Wang N, Jones JB, Sundin GW et al (eds) Virulence mechanisms of plant-pathogenic bacteria. Bacteriology. The American Phytopathological Society, St. Paul, pp 107–124. CrossRefGoogle Scholar
  14. 14.
    Hormaeche I, Segura RL, Vecino AJ, Goñi FM, de la Cruz F, Alkorta I (2006) The transmembrane domain provides nucleotide binding specificity to the bacterial conjugation protein TrwB. FEBS Lett 580(13):3075–3082. CrossRefPubMedGoogle Scholar
  15. 15.
    Kanchan K, Linder J, Winkler K, Hantke K, Schultz A, Schultz JE (2010) Transmembrane signaling in chimeras of the Escherichia coli aspartate and serine chemotaxis receptors and bacterial class III adenylyl cyclases. J Biol Chem 285(3):2090–2099. CrossRefPubMedGoogle Scholar
  16. 16.
    Taylor BL, Zhulin IB (1999) PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol Mol Biol Rev 63(2):479–506CrossRefGoogle Scholar
  17. 17.
    Gilles-Gonzalez M-A, Gonzalez G (2004) Signal transduction by heme-containing PAS-domain proteins. J Appl Physiol 96(2):774–783. CrossRefPubMedGoogle Scholar
  18. 18.
    Chang AL, Tuckerman JR, Gonzalez G, Mayer R, Weinhouse H, Volman G, Amikam D, Benziman M, Gilles-Gonzalez M-A (2001) Phosphodiesterase a1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 40(12):3420–3426. CrossRefPubMedGoogle Scholar
  19. 19.
    Delgado-Nixon VM, Gonzalez G, Gilles-Gonzalez M-A (2000) Dos, a heme-binding pas protein from Escherichia coli, is a direct oxygen sensor. Biochemistry 39(10):2685–2691. CrossRefPubMedGoogle Scholar
  20. 20.
    Bekker M, Teixeira de Mattos MJ, Hellingwerf KJ (2006) The role of two-component regulation systems in the physiology of the bacterial cell. Sci Prog 89(Pt 3–4):213–242CrossRefGoogle Scholar
  21. 21.
    Heikaus CC, Pandit J, Klevit RE (2009) Cyclic nucleotide binding GAF domains from phosphodiesterases: structural and mechanistic insights. Structure 17(12):1551–1557. CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Anantharaman V, Aravind L (2001) The chase domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem Sci 26(10):579–582. CrossRefPubMedGoogle Scholar
  23. 23.
    Pas J, von Grotthuss M, Wyrwicz LS, Rychlewski L, Barciszewski J (2004) Structure prediction, evolution and ligand interaction of Chase domain. FEBS Lett 576(3):287–290. CrossRefPubMedGoogle Scholar
  24. 24.
    Anantharaman V, Aravind L (2000) Cache – a signaling domain common to animal ca2+-channel subunits and a class of prokaryotic chemotaxis receptors. Trends Biochem Sci 25(11):535–537. CrossRefPubMedGoogle Scholar
  25. 25.
    Galperin MY, Gaidenko TA, Mulkidjanian AY, Nakano M, Price CW (2001) MhyT, a new integral membrane sensor domain. FEMS Microbiol Lett 205(1):17–23. CrossRefPubMedGoogle Scholar
  26. 26.
    Nikolskaya AN, Mulkidjanian AY, Beech IB, Galperin MY (2003) Mase1 and Mase2: two novel integral membrane sensory domains. J Mol Microbiol Biotechnol 5(1):11–16. CrossRefPubMedGoogle Scholar
  27. 27.
    Williams P (2007) Quorum sensing, communication and cross-kingdom signalling in the bacterial world. Microbiology 153(Pt 12):3923–3938. CrossRefPubMedGoogle Scholar
  28. 28.
    He Y-W, Zhang L-H (2008) Quorum sensing and virulence regulation in Xanthomonas campestris. FEMS Microbiol Rev 32(5):842–857. CrossRefPubMedGoogle Scholar
  29. 29.
    Whiteley M, Diggle SP, Greenberg EP (2017) Progress in and promise of bacterial quorum sensing research. Nature 551:313. CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Deng Y, Wu J, Tao F, Zhang L-H (2011) Listening to a new language: DSF-based quorum sensing in gram-negative bacteria. Chem Rev 111(1):160–173. CrossRefPubMedGoogle Scholar
  31. 31.
    Zhou L, Zhang L-H, Cámara M, He Y-W (2017) The DSF family of quorum sensing signals: diversity, biosynthesis, and turnover. Trends Microbiol 25(4):293–303. CrossRefPubMedGoogle Scholar
  32. 32.
    Tang J-L, Liu Y-N, Barber CE, Dow JM, Wootton JC, Daniels MJ (1991) Genetic and molecular analysis of a cluster of rpf genes involved in positive regulation of synthesis of extracellular enzymes and polysaccharide in Xanthomonas campestris pathovar campestris. Mol Gen Genet MGG 226(3):409–417. CrossRefPubMedGoogle Scholar
  33. 33.
    Cheng Z, He Y-W, Lim SC, Qamra R, Walsh MA, Zhang L-H, Song H (2010) Structural basis of the sensor-synthase interaction in autoinduction of the quorum sensing signal DSF biosynthesis. Structure 18(9):1199–1209. CrossRefPubMedGoogle Scholar
  34. 34.
    Zhou L, Yu Y, Chen X, Diab AA, Ruan L, He J, Wang H, He YW (2015) The multiple DSF-family qs signals are synthesized from carbohydrate and branched-chain amino acids via the FAS elongation cycle. Sci Rep 5:13294. CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    He Y-W, Wang C, Zhou L, Song H, Dow JM, Zhang L-H (2006) Dual signaling functions of the hybrid sensor kinase RpfC of Xanthomonas campestris involve either phosphorelay or receiver domain-protein interaction. J Biol Chem 281(44):33414–33421. CrossRefPubMedGoogle Scholar
  36. 36.
    Cai Z, Yuan Z-H, Zhang H, Pan Y, Wu Y, Tian X-Q, Wang F-F, Wang L, Qian W (2017) Fatty acid DSF binds and allosterically activates histidine kinase Rpfc of phytopathogenic bacterium Xanthomonas campestris pv. campestris to regulate quorum-sensing and virulence. PLoS Pathog 13(4):e1006304. CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Ryan RP, Fouhy Y, Lucey JF, Dow JM (2006) Cyclic di-GMP signaling in bacteria: recent advances and new puzzles. J Bacteriol 188(24):8327–8334. CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    He Y-W, Ng AY-J, Xu M, Lin K, Wang L-H, Dong Y-H, Zhang L-H (2007) Xanthomonas campestris cell–cell communication involves a putative nucleotide receptor protein Clp and a hierarchical signalling network. Mol Microbiol 64(2):281–292. CrossRefPubMedGoogle Scholar
  39. 39.
    Ryan RP, McCarthy Y, Andrade M, Farah CS, Armitage JP, Dow JM (2010) Cell–cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris. Proc Natl Acad Sci USA 107(13):5989–5994. CrossRefPubMedGoogle Scholar
  40. 40.
    Ryan RP, McCarthy Y, Kiely PA, O’Connor R, Farah CS, Armitage JP, Dow JM (2012) Dynamic complex formation between HD-GYP, GGDEF and PilZ domain proteins regulates motility in Xanthomonas campestris. Mol Microbiol 86(3):557–567. CrossRefPubMedGoogle Scholar
  41. 41.
    Zhang LH (2010) A novel c-di-GMP effector linking intracellular virulence regulon to quorum sensing and hypoxia sensing. Virulence 1(5):391–394. CrossRefPubMedGoogle Scholar
  42. 42.
    He Y-W, Boon C, Zhou L, Zhang L-H (2009) Co-regulation of Xanthomonas campestris virulence by quorum sensing and a novel two-component regulatory system RavS/RavR. Mol Microbiol 71(6):1464–1476. CrossRefPubMedGoogle Scholar
  43. 43.
    Tao J, Li C, Luo C, He C (2014) Rava/RavR two-component system regulates Xanthomonas campestris pathogenesis and c-di-GMP turnover. FEMS Microbiol Lett 358(1):81–90. CrossRefPubMedGoogle Scholar
  44. 44.
    Ryan RP, Fouhy Y, Lucey JF, Jiang B-L, He Y-Q, Feng J-X, Tang J-L, Dow JM (2007) Cyclic di-GMP signalling in the virulence and environmental adaptation of Xanthomonas campestris. Mol Microbiol 63(2):429–442. CrossRefPubMedGoogle Scholar
  45. 45.
    Hsiao Y-M, Liu Y-F, Fang M-C, Song W-L (2011) Xcc2731, a GGDEF domain protein in Xanthomonas campestris, is involved in bacterial attachment and is positively regulated by Clp. Microbiol Res 166(7):548–565. CrossRefPubMedGoogle Scholar
  46. 46.
    Hsiao Y-M, Song W-L, Liao C-T, Lin I-H, Pan M-Y, Lin C-F (2012) Transcriptional analysis and functional characterization of Xcc1294 gene encoding a GGDEF domain protein in Xanthomonas campestris pv. campestris. Arch Microbiol 194(4):293–304. CrossRefPubMedGoogle Scholar
  47. 47.
    Hengge R (2009) Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 7:263. CrossRefPubMedGoogle Scholar
  48. 48.
    de Crecy-Lagard V, Glaser P, Lejeune P, Sismeiro O, Barber CE, Daniels MJ, Danchin A (1990) A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity. J Bacteriol 172(10):5877–5883. CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Chin K-H, Lee Y-C, Tu Z-L, Chen C-H, Tseng Y-H, Yang J-M, Ryan RP, McCarthy Y, Dow JM, Wang AHJ, Chou S-H (2010) The cAMP receptor-like protein Clp is a novel c-di-GMP receptor linking cell–cell signaling to virulence gene expression in Xanthomonas campestris. J Mol Biol 396(3):646–662. CrossRefPubMedGoogle Scholar
  50. 50.
    Leduc JL, Roberts GP (2009) Cyclic di-GMP allosterically inhibits the CRP-like protein (clp) of Xanthomonas axonopodis pv. citri. J Bacteriol 191(22):7121–7122. CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Tao F, He Y-W, Wu D-H, Swarup S, Zhang L-H (2010) The cyclic nucleotide monophosphate domain of Xanthomonas campestris global regulator Clp defines a new class of cyclic di-GMP effectors. J Bacteriol 192(4):1020–1029. CrossRefPubMedGoogle Scholar
  52. 52.
    Chou SH (2011) Delicate conformational changes of a protein in the CRP family lead to dramatic functional changes via binding of an alternate secondary messenger molecule. Virulence 2(2):152–157CrossRefGoogle Scholar
  53. 53.
    Saveanu C, Miron S, Borza T, Craescu CT, Labesse G, Gagyi C, Popescu A, Schaeffer F, Namane A, Laurent-Winter C, Bârzu O, Gilles A-M (2002) Structural and nucleotide-binding properties of YajQ and YnaF, two Escherichia coli proteins of unknown function. Protein Sci 11(11):2551–2560. CrossRefPubMedPubMedCentralGoogle Scholar
  54. 54.
    An S-q, Caly DL, McCarthy Y, Murdoch SL, Ward J, Febrer M, Dow JM, Ryan RP (2014) Novel cyclic di-GMP effectors of the yajq protein family control bacterial virulence. PLoS Pathol 10(10):e1004429. CrossRefGoogle Scholar
  55. 55.
    Zhao Z, Wu Z, Zhang J (2016) Crystal structure of the YajQ-family protein Xc_3703 from Xanthomonas campestris pv. campestris. Acta Crystallogr F Struct Biol Commun 72(Pt 9):720–725. CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Amikam D, Galperin MY (2006) PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 22(1):3–6. CrossRefPubMedGoogle Scholar
  57. 57.
    Habazettl J, Allan MG, Jenal U, Grzesiek S (2011) Solution structure of the PilZ domain protein PA4608 complex with cyclic di-GMP identifies charge clustering as molecular readout. J Biol Chem 286(16):14304–14314. CrossRefPubMedPubMedCentralGoogle Scholar
  58. 58.
    Mccarthy Y, Ryan RP, O’donovan K, He Y-Q, Jiang B-L, Feng J-X, Tang J-L, Dow JM (2008) The role of PilZ domain proteins in the virulence of Xanthomonas campestris pv. campestris. Mol Plant Pathol 9(6):819–824. CrossRefPubMedPubMedCentralGoogle Scholar
  59. 59.
    Li TN, Chin KH, Shih HL, Wang AH, Chou SH (2009) Crystallization and preliminary X-ray diffraction characterization of an essential protein from Xanthomonas campestris that contains a noncanonical PilZ signature motif yet is critical for pathogenicity. Acta Crystallogr Sect F Struct Biol Cryst Commun 65(Pt 10):1056–1059. CrossRefPubMedPubMedCentralGoogle Scholar
  60. 60.
    Guzzo CR, Salinas RK, Andrade MO, Farah CS (2009) PilZ protein structure and interactions with PilB and the FimX EAL domain: implications for control of type IV pilus biogenesis. J Mol Biol 393(4):848–866. CrossRefPubMedGoogle Scholar
  61. 61.
    Liao YT, Chin KH, Kuo WT, Chuah ML, Liang ZX, Chou SH (2012) Crystallization and preliminary X-ray diffraction characterization of the XccFimX(EAL)-c-di-GMP and XccFimX(EAL)-c-di-GMP-XccPilZ complexes from Xanthomonas campestris. Acta Crystallogr Sect F Struct Biol Cryst Commun 68(Pt 3):301–305. CrossRefPubMedPubMedCentralGoogle Scholar
  62. 62.
    Li T-N, Chin K-H, Fung K-M, Yang M-T, Wang AHJ, Chou S-H (2011) A novel tetrameric PilZ domain structure from xanthomonads. PLoS One 6(7):e22036. CrossRefPubMedPubMedCentralGoogle Scholar
  63. 63.
    Li T-N, Chin K-H, Liu J-H, Wang AH-J, Chou S-H (2009) Xc1028 from Xanthomonas campestris adopts a PilZ domain-like structure without a c-di-GMP switch. Proteins 75(2):282–288. CrossRefPubMedGoogle Scholar

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Authors and Affiliations

  1. 1.Shanghai Jiao Tong UniversityShanghaiPeople’s Republic of China
  2. 2.Institute of MicrobiologyChinese Academy of SciencesBeijingPeople’s Republic of China
  3. 3.Institute of Biochemistry and Agricultural Biotechnology CenterNational Chung Hsing UniversityTaichungTaiwan
  4. 4.State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanPeople’s Republic of China

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